My first choice would be Cloud and Tifa - to me their relationship was the deepest, most complex and well-contructed relationship in the series.
A close second is Zidane and Garnet...you saw it coming from MILES away but Garnet at least played hard to get.
Tidus and Yuna were very cute, and
SPOILER!!:
it was very tragic the way they were parted at the end
but yeah X-2 ruined all that...
Locke and Celes didn't really strike a chord with me..perhaps I never really took much notice of them, I was more concerned by
SPOILER!!:
Locke's freakish desire to keep his dead girlfriend preserved in a basement! Who knows what that creepy old man was up to when he wasn't around...
. So that kind of detracted from the "ahh cute" factor for me.
Cecil and Rosa...meh...Cute and committed, it was pretty established and not really dealt with too deeply in the storyline (in the SNES and GBA versions at least). I haven't played the DS version yet so I'm not sure if it goes into the dynamics of their relationship a bit more.
Did I mention Squall and Rinoa? I didn't? Oh....lol. That about sums it up I didn't mind their coupling but it did not have any major appeal to me. Bringing him out his shell was all very cute and heartening, I suppose it had its moments...